Updating Examples in Documentation

[jaronoff14]

Description

Updated the example in integrate.py to comply with the current hoomd syntax and converted examples in hoomd/md so that they are tested with Sybil

Motivation and context

The old example in integrate.py was from an older version of hoomd and the syntax was not functional in the current version of hoomd

Partially Resolves #1958
I am not sure if this catches all of the old examples

How has this been tested?

The example in integrate.py was tested by following the tutorials in a jupyter notebook.
The sphinx documentation was rebuilt.

Checklist:

• [ x] I have reviewed the Contributor Guidelines.

• [x ] I agree with the terms of the HOOMD-blue Contributor Agreement.

• My name is on the list of contributors (sphinx-doc/credits.rst) in the pull request source branch.

• I have summarized these changes in CHANGELOG.rst following the established format.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[joaander]

Sorry for the delay, I will review this soon.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[github-actions]

This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

[joaander]

Thanks! And sorry for the long delay before reviewing this.

I pushed commits that fix the errors in all the code examples that are tested by this PR. I am going to merge now so that I can include this in the next release. However, I would still like to add your name and affiliation to credit your contribution. Let me know that information in a comment and I will add it to the documentation.

[jaronoff14]

No worries on the delay.
Jon Aronoff, University of Utah

[joaander]

Thanks again!